Introduction

Biophotonics Discovery requires authors to make all data necessary to replicate their study’s findings publicly available without restriction at the time of submission. When specific legal or ethical restrictions prohibit public sharing of a data set, authors must indicate how others may obtain access to the data.

When submitting a manuscript, authors must include a Code and Data Availability Statement describing compliance with the journal’s data policy in a section following the Disclosures. If the article is accepted for publication, the Code and Data Availability Statement will be published as part of the article. Acceptable data sharing methods are listed below.

Data availability allows and facilitates:

• Validation, replication, reanalysis, new analysis, reinterpretation or inclusion into meta-analyses;
• Reproducibility of research;
• Efforts to ensure data are archived, increasing the value of the investment made in funding scientific research;
• Reduction of the burden on authors in preserving and finding old data, and managing data access requests;
• Citation and linking of research data and their associated articles, enhancing visibility and ensuring recognition for authors, data producers and curators.

Publication in Biophotonics Discovery is conditional on compliance with this policy. If restrictions on access to data come to light after publication, we reserve the right to post a Correction, an Editorial Expression of Concern, contact the authors' institutions and funders, or, in extreme cases, retract the publication.

Minimal Data Set Definition

Authors must share the “minimal data set” for their submission. BIOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods. Additionally, BIOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data when applicable.

For example, authors should submit the following data:

• The values behind the means, standard deviations and other measures reported;
• The values used to build graphs;
• The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. Also, authors do not need to submit the raw data collected during an investigation if the standard in the field is to share data that have been processed.

BIOS does not permit references to “data not shown.” Authors should deposit relevant data in a public data repository or provide the data in the manuscript.

We require authors to provide sample image data in support of all reported results either with the submission files or in a public repository.

When reviewing concerns arising after publication in relation to images shown, we may request available underlying data for any image files depicted in the article, as needed to resolve the concern(s).

Acceptable Data Sharing Methods

Data in Supporting Information Files

In many cases data can be published with the article as supplemental content. Supplemental content files can be accessed by readers with the published article. When including data as supplemental content, authors should submit data in a file format from which data can be efficiently extracted (for example, spreadsheets are preferable to PDFs or images when providing tabulated data).

Supplemental content files are published exactly as provided and are not copyedited. Each file should be less than 100 MB. The maximum file size for all files, including the article, figures, tables, and supplemental data, is 450 MB.

Deposition within data repository

Data can also be deposited in appropriate public data repositories, unless already provided as part of a submitted article. Repositories may be either subject-specific repositories that accept specific types of structured data, or cross-disciplinary generalist repositories that accept multiple data types.

The Data Availability Statement must list the name of the repository or repositories as well as digital object identifiers (DOIs), accession numbers or codes, or other persistent identifiers for all relevant data.

Data citation

When applicable, BIOS encourages authors to cite any publicly available research data in their reference list. References to data sets (data citations) must include a persistent identifier (such as a DOI) and follow journal style.

Example:
C. Andrikou, D. Thiel, J. A. Ruiz-Santiesteban, and A. Hejnol, "Active mode of excretion across digestive tissues predates the origin of excretory organs," Dryad Digital Repository (2019) https://doi.org/10.5061/dryad.bq068jr

Acceptable Data Access Restrictions

BIOS recognizes that, in some instances, authors may not be able to make their underlying data set publicly available for legal or ethical reasons. This data policy does not overrule local regulations, legislation, or ethical frameworks. Where these frameworks prevent or limit data release, authors must make these limitations clear in the Data Availability Statement at the time of submission. Acceptable restrictions on public data sharing are detailed below.

Please note it is not acceptable for an author to be the sole named individual responsible for ensuring data access.

Third-party data

For studies involving third-party data, we encourage authors to share any data specific to their analyses that they can legally distribute. We recognize, however, that authors may be using third-party data they do not have the rights to share. When third-party data cannot be publicly shared, authors must provide all information necessary for interested researchers to apply to gain access to the data.

For any third-party data that the authors cannot legally distribute, they should include the following information in their Data Availability Statement upon submission:

• A description of the data set and the third-party source
• If applicable, verification of permission to use the data set
• All necessary contact information others would need to apply to gain access to the data

Authors should properly cite and acknowledge the data source in the manuscript. Please note, if data have been obtained from a third-party source, we require that other researchers would be able to access the data set in the same manner as the authors.

Human research participant data and other sensitive data

For studies involving human research participant data or other sensitive data, we encourage authors to share de-identified or anonymized data. However, when data cannot be publicly shared, we allow authors to make their data sets available upon request.

If there are ethical or legal restrictions on sharing a sensitive data set, authors should provide the following information within their Data Availability Statement upon submission:

• Explain the restrictions in detail (e.g., data contain potentially identifying or sensitive patient information)
• Provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent

General guidelines for human research participant data

Prior to sharing human research participant data, authors should consult with an ethics committee to ensure data are shared in accordance with participant consent and all applicable local laws.

Data sharing should never compromise participant privacy. It is therefore not appropriate to publicly share personally identifiable data on human research participants. The following are examples of data that should not be shared: 

• Name, initials, physical address
• Internet protocol (IP) address
• Specific dates (birth dates, death dates, examination dates, etc.)
• Contact information such as phone number or email address
• Location data

Data that are not directly identifying may also be inappropriate to share, as in combination they can become identifying. For example, data collected from a small group of participants, vulnerable populations, or private groups should not be shared if they involve indirect identifiers (such as sex, ethnicity, location, etc.) that may risk the identification of study participants. 

Steps necessary to protect privacy may include de-identifying data, adding noise, or blocking portions of the database.

Additional help

Please contact the journal office (BIOS@spie.org) if:

• You have concerns about the ethics or legality of sharing your data
• You feel unable to share data for reasons not specified above

Unacceptable Data Access Restrictions

Biophotonics Discovery will not consider manuscripts for which the following factors influence authors’ ability to share data:

• Authors will not share data because of personal interests, such as patents or potential future publications.
• The conclusions depend solely on the analysis of proprietary data. We consider proprietary data to be data owned by individuals, organizations, funders, institutions, commercial interests, or other parties that the data owners will not share. If proprietary data are used and cannot be accessed by others in the same manner by which the authors obtained them, the manuscript must include an analysis of publicly available data that validates the study’s conclusions so that others can reproduce the analysis and build on the study’s findings.

FAQs

What if my article does not contain any data?

All articles must include a Data Availability Statement, but some submissions, such as Review papers or Perspectives, may not contain data. For manuscripts that do not report data, authors must state in their Data Availability Statement that their article does not report data and the data availability policy is not applicable to their article.

What if I cannot provide accession numbers or DOIs for my data set at submission?

Authors may submit their manuscript and include placeholder language in their Data Availability Statement indicating that accession numbers and/or DOIs will be made available after acceptance. The journal office will contact authors prior to publication to ask for this information and will hold the paper until it is received. Providing private data access to reviewers and editors during the peer review process is acceptable. Many repositories permit private access for review purposes, and have policies for public release at publication.

I cannot afford the cost of depositing a large amount of data to a third-party repository. What should I do?

BIOS encourages authors to investigate all options and to contact their institutions if they have difficulty providing access to the data underlying the research.

What are acceptable licenses for my data deposition?

If authors use repositories with stated licensing policies, the policies should not be more restrictive than the Creative Commons Attribution (CC BY) license.

 

Research Resource Identifiers (RRIDs)

We encourage authors to use Research Resource Identifiers (RRIDs) to cite key resources such as antibodies, model organisms, cell lines, and tools (e.g., software, databases) used in their research. RRIDs help improve resource identification, discovery, and reuse, promoting reproducibility in science. 

To obtain RRIDs, authors should:

1. Visit the Resource Identification Portal.
2. Search for the resource and click “Cite This” to get the citation.
3. If the resource is not found, register it through the portal.

For assistance, contact rii-help@scicrunch.org.

Example Citations:

• Antibodies: “Wnt3 was localized using a rabbit polyclonal antibody C64F2 (Cell Signaling Technology, Cat# 2721S, RRID: AB_2215411)”
• Model Organisms: “Experiments were conducted in C. elegans strain SP304 (RRID:CGC_SP304)”
• Cell Lines: “Experiments were conducted in PC12 CLS cells (CLS Cat# 500311/p701_PC-12, RRID: CVCL_0481)”
• Tools, Software, and Databases: “Image analysis was conducted with CellProfiler Image Analysis Software, V2.0 (RRID: nif-0000-00280)”

Sharing Software

We encourage authors to make all relevant algorithms and software freely available.

Code can be shared as a supplement or using any well-known repositories, including FigShare, Github, and CodeOcean. Data or code contained in an external repository should be cited in the reference list, and authors should include a DOI or other persistent identifier.

Dataset Reference Example: Creator Name, “Dataset Title,” Repository Name, version (publication year). https://doi.org/.....

Manuscripts that include externally hosted code should mention that code and the name of the repository in the text of the paper or figure caption:

Example 1:
The archived version of the code can be freely accessed and executed through Code Ocean.

Example 2:
The code used to generate the results and figures is available in a Github repository.

Code Ocean is our recommended platform for sharing code, but other repositories may be similarly used as a hosting platform. Software and code essential for reproducibility and reuse can be easily incorporated into your SPIE journal manuscript via Code Ocean.

Authors of papers that mention code/software on Code Ocean will receive instructions on how to link the code to the article in the author proofs.

In the case that the software is the central focus of the manuscript (e.g. for manuscripts describing an open source code), it is expected that authors will make all relevant software available without restrictions upon publication of the work, while adhering to the following requirements:

• Based on open source standards
• Conform to the Open Source Definition
• Deposited in an open software archive
• Included in the submission as supporting information
• Linked directly from the manuscript file.